/dports/textproc/fox-xml/fox-4.1.2-91-g9c6716e/wcml/ |
H A D | m_wcml_molecule.F90 | 366 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i))) 409 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i))) 454 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i))) 500 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i))) 543 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i))) 586 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i))) 631 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i))) 677 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i))) 1083 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i))) 1126 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i))) [all …]
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H A D | m_wcml_molecule.m4 | 37 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i))) 49 if (present(atomIds)) call xml_AddAttribute(xf, "id", trim(atomIds(i))) 62 character(len=*), intent(in), optional :: atomIds(:) 81 if (present(atomIds)) then 125 if (present(atomIds)) then 151 character(len=*), intent(in), optional :: atomIds(:) 170 if (present(atomIds)) then 216 if (present(atomIds)) then 237 character(len=*), intent(in), optional :: atomIds(:) 288 character(len=*), intent(in), optional :: atomIds(:) [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/ |
H A D | AllChem.py | 111 def GetConformerRMS(mol, confId1, confId2, atomIds=None, prealigned=False): argument 131 if atomIds: 132 AlignMolConformers(mol, confIds=[confId1, confId2], atomIds=atomIds) 147 def GetConformerRMSMatrix(mol, atomIds=None, prealigned=False): argument 179 if atomIds: 180 AlignMolConformers(mol, atomIds=atomIds, RMSlist=rmsvals) 186 GetConformerRMS(mol, confIds[0], confIds[i], atomIds=atomIds, prealigned=prealigned)) 192 cmat.append(GetConformerRMS(mol, confIds[i], confIds[j], atomIds=atomIds, prealigned=True))
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/dports/science/rdkit/rdkit-Release_2021_03_5/Contrib/IFG/ |
H A D | README | 18 # return the list of IFG (atomIds, atoms & type) for a molecule object: 24 [IFG(atomIds=(2,), atoms='n', type='cnc'), 25 IFG(atomIds=(4, 5, 6, 7), atoms='NS(=O)=O', type='cNS(c)(=O)=O'), 26 IFG(atomIds=(12,), atoms='N', type='cN'), 27 IFG(atomIds=(15,), atoms='n', type='cnc')]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolAlign/ |
H A D | AlignMolecules.cpp | 191 const std::vector<unsigned int> *atomIds = nullptr) { in _fillAtomPositions() argument 194 if (atomIds == nullptr) { in _fillAtomPositions() 201 pts.reserve(atomIds->size()); in _fillAtomPositions() 203 for (cai = atomIds->begin(); cai != atomIds->end(); cai++) { in _fillAtomPositions() 209 void alignMolConformers(ROMol &mol, const std::vector<unsigned int> *atomIds, in alignMolConformers() argument 224 _fillAtomPositions(refPoints, refCnf, atomIds); in alignMolConformers() 239 _fillAtomPositions(prbPoints, *(*cnfi), atomIds); in alignMolConformers() 257 _fillAtomPositions(prbPoints, conf, atomIds); in alignMolConformers()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Descriptors/ |
H A D | USRDescriptor.cpp | 162 std::vector<std::vector<unsigned int>> &atomIds) { in getAtomIdsForFeatures() argument 164 PRECONDITION(atomIds.size() == numFeatures, in getAtomIdsForFeatures() 178 atomIds[i].push_back(mi.second); in getAtomIdsForFeatures() 215 std::vector<std::vector<unsigned int>> &atomIds, int confId) { in USRCAT() argument 227 unsigned int numClasses = atomIds.size(); in USRCAT() 230 atomIds.resize(numClasses); in USRCAT() 231 getAtomIdsForFeatures(mol, atomIds); in USRCAT() 252 for (const auto &atomsInClass : atomIds) { in USRCAT()
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/dports/math/vtk9/VTK-9.1.0/Domains/Chemistry/ |
H A D | vtkMoleculeMapper.cxx | 244 vtkSelection* selection, vtkIdTypeArray* atomIds, vtkIdTypeArray* bondIds) in GetSelectedAtomsAndBonds() argument 247 if (selection == nullptr || (atomIds == nullptr && bondIds == nullptr)) in GetSelectedAtomsAndBonds() 253 if (atomIds != nullptr) in GetSelectedAtomsAndBonds() 255 atomIds->Reset(); in GetSelectedAtomsAndBonds() 285 if (atomIds != nullptr && curId < numAtoms) // atoms in GetSelectedAtomsAndBonds() 287 atomIds->InsertNextValue(curId); in GetSelectedAtomsAndBonds() 642 vtkIdType atomIds[2]; in UpdateBondGlyphPolyData() local 657 atomIds[0] = bond.GetBeginAtomId(); in UpdateBondGlyphPolyData() 658 atomIds[1] = bond.GetEndAtomId(); in UpdateBondGlyphPolyData() 761 cylColors->InsertNextTuple(atomIds[0], atomColorArray); in UpdateBondGlyphPolyData() [all …]
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H A D | vtkMoleculeMapper.h | 263 vtkSelection* selection, vtkIdTypeArray* atomIds, vtkIdTypeArray* bondIds); 264 virtual void GetSelectedAtoms(vtkSelection* selection, vtkIdTypeArray* atomIds) in GetSelectedAtoms() argument 266 this->GetSelectedAtomsAndBonds(selection, atomIds, nullptr); in GetSelectedAtoms()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/MinimalLib/ |
H A D | jswrapper.cpp | 25 std::vector<int> &atomIds, 58 std::vector<int> atomIds; in draw_to_canvas_with_highlights() local 69 atomIds, bondIds); in draw_to_canvas_with_highlights() 80 MolDraw2DUtils::prepareAndDrawMolecule(*d2d, *self.d_mol, legend, &atomIds, in draw_to_canvas_with_highlights()
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H A D | minilib.cpp | 45 std::string &legend, std::vector<int> &atomIds, in process_details() argument 57 atomIds.push_back(molval.GetInt()); in process_details() 148 std::vector<int> atomIds; in svg_() local 154 atomIds, bondIds); in svg_() 166 MolDraw2DUtils::prepareAndDrawMolecule(drawer, m, legend, &atomIds, &bondIds); in svg_()
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/dports/math/vtk6/VTK-6.2.0/Domains/Chemistry/ |
H A D | vtkMoleculeMapper.h | 193 vtkIdTypeArray *atomIds, 196 vtkIdTypeArray *atomIds) in GetSelectedAtoms() argument 198 this->GetSelectedAtomsAndBonds(selection, atomIds, NULL); in GetSelectedAtoms()
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H A D | vtkMoleculeMapper.cxx | 226 vtkIdTypeArray *atomIds, in GetSelectedAtomsAndBonds() argument 230 if (selection == NULL || (atomIds == NULL && bondIds == NULL) ) in GetSelectedAtomsAndBonds() 236 if (atomIds != NULL) in GetSelectedAtomsAndBonds() 238 atomIds->Reset(); in GetSelectedAtomsAndBonds() 269 if (atomIds != NULL && curId < numAtoms) // atoms in GetSelectedAtomsAndBonds() 271 atomIds->InsertNextValue(curId); in GetSelectedAtomsAndBonds()
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/dports/math/vtk8/VTK-8.2.0/Domains/Chemistry/ |
H A D | vtkMoleculeMapper.h | 256 vtkIdTypeArray *atomIds, 259 vtkIdTypeArray *atomIds) in GetSelectedAtoms() argument 261 this->GetSelectedAtomsAndBonds(selection, atomIds, nullptr); in GetSelectedAtoms()
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H A D | vtkMoleculeMapper.cxx | 245 vtkIdTypeArray *atomIds, in GetSelectedAtomsAndBonds() argument 249 if (selection == nullptr || (atomIds == nullptr && bondIds == nullptr) ) in GetSelectedAtomsAndBonds() 255 if (atomIds != nullptr) in GetSelectedAtomsAndBonds() 257 atomIds->Reset(); in GetSelectedAtomsAndBonds() 288 if (atomIds != nullptr && curId < numAtoms) // atoms in GetSelectedAtomsAndBonds() 290 atomIds->InsertNextValue(curId); in GetSelectedAtomsAndBonds()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Wrap/ |
H A D | StereoGroup.cpp | 31 python::object atomIds) { in createStereoGroup() argument 33 python::stl_input_iterator<unsigned int> beg(atomIds), end; in createStereoGroup()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Subgraphs/ |
H A D | SubgraphUtils.cpp | 112 PATH_TYPE bondListFromAtomList(const ROMol &mol, const PATH_TYPE &atomIds) { in bondListFromAtomList() argument 114 unsigned int natms = atomIds.size(); in bondListFromAtomList() 120 const Bond *bnd = mol.getBondBetweenAtoms(atomIds[i], atomIds[j]); in bondListFromAtomList()
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/dports/math/vtk9/VTK-9.1.0/Rendering/RayTracing/ |
H A D | vtkOSPRayMoleculeMapperNode.cxx | 220 vtkIdType atomIds[2]; in Render() local 239 atomIds[0] = bond.GetBeginAtomId(); in Render() 240 atomIds[1] = bond.GetEndAtomId(); in Render() 259 materials.emplace_back(_elementMaterials[atomicNumbers->GetValue(atomIds[0])]); in Render() 266 materials.emplace_back(_elementMaterials[atomicNumbers->GetValue(atomIds[1])]); in Render()
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/io/ |
H A D | cmlformat.cpp | 186 atomIds[std::string(attribute.value())] = atom.index(); in atoms() 264 begin = atomIds.find(tokens[0]); in bonds() 265 end = atomIds.find(tokens[1]); in bonds() 266 if (begin != atomIds.end() && end != atomIds.end() && in bonds() 403 std::map<std::string, Index> atomIds; member in Avogadro::Io::__anonbe0cb7170211::CmlFormatPrivate
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/io/ |
H A D | cmlformat.cpp | 186 atomIds[std::string(attribute.value())] = atom.index(); in atoms() 264 begin = atomIds.find(tokens[0]); in bonds() 265 end = atomIds.find(tokens[1]); in bonds() 266 if (begin != atomIds.end() && end != atomIds.end() && in bonds() 403 std::map<std::string, Index> atomIds; member in Avogadro::Io::__anon5d3274410211::CmlFormatPrivate
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/dports/science/openbabel/openbabel-3.1.1/src/formats/xml/ |
H A D | cmlformat.cpp | 1522 vector<string> atomIds; in WriteMolecule() local 1579 id << " " << atomIds[patom->GetIdx()]; in WriteMolecule() 1827 ref1 = atomIds[pbond->GetBeginAtomIdx()]; in WriteMolecule() 1828 ref2 = atomIds[pbond->GetEndAtomIdx()]; in WriteMolecule() 1858 atomrefs[0] = atomIds[mol.GetAtomById(beginref)->GetIdx()]; in WriteMolecule() 1859 atomrefs[1] = atomIds[mol.GetAtomById(ct_cfg.begin)->GetIdx()]; in WriteMolecule() 1860 atomrefs[2] = atomIds[mol.GetAtomById(ct_cfg.end)->GetIdx()]; in WriteMolecule() 1861 atomrefs[3] = atomIds[mol.GetAtomById(endref)->GetIdx()]; in WriteMolecule() 1900 ref1 += ' ' + atomIds[pbond->GetBeginAtomIdx()]; in WriteMolecule() 1901 ref2 += ' ' + atomIds[pbond->GetEndAtomIdx()]; in WriteMolecule() [all …]
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/qtplugins/editor/ |
H A D | editor.cpp | 275 Core::Array<Index> atomIds; in reset() local 276 atomIds.push_back(a3); in reset() 277 atomIds.push_back(a2); in reset() 278 atomIds.push_back(a1); in reset() 281 m_molecule->adjustHydrogens(atomIds); in reset()
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/qtplugins/editor/ |
H A D | editor.cpp | 275 Core::Array<Index> atomIds; in reset() local 276 atomIds.push_back(a3); in reset() 277 atomIds.push_back(a2); in reset() 278 atomIds.push_back(a1); in reset() 281 m_molecule->adjustHydrogens(atomIds); in reset()
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/dports/textproc/fox-xml/fox-4.1.2-91-g9c6716e/wcml/test/ |
H A D | test_cmlAddMolecule_12.f90 | 24 atomIds=(/"c1", "o1", "h1", "h2"/), bondAtom1Refs=(/"c1", "c1", "c1"/), &
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H A D | test_cmlAddMolecule_13.f90 | 24 atomIds=(/"c1", "o1", "h1", "h2"/), bondAtom1Refs=(/"c1", "c1", "c1", "c1"/), &
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H A D | test_cmlAddMolecule_9.f90 | 24 atomIds=(/"c1", "o1", "h1", "h2"/), bondAtom1Refs=(/"c1", "c1", "c1"/), &
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